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Cross-tissue immune cell analysis reveals tissue-specific features in humans

Authors
C. Domínguez Conde,C. Xu
L. B. Jarvis,D. B. Rainbow,S. B. Wells,T. Gomes,S. K. Howlett,O. Suchanek,K. Polanski,H. W. King,L. Mamanova,N. Huang,P. A. Szabo,L. Richardson,L. Bolt,E. S. Fasouli,K. T. Mahbubani,M. Prete,L. Tuck,N. Richoz,Z. K. Tuong,L. Campos,H. S. Mousa,E. J. Needham,S. Pritchard,T. Li,R. Elmentaite,J. Park,E. Rahmani,D. Chen,D. K. Menon,O. A. Bayraktar,L. K. James,K. B. Meyer,N. Yosef,M. R. Clatworthy,P. A. Sims,D. L. Farber,K. Saeb-Parsy,J. L. Jones,S. A. Teichmann,Cecilia Conde,Liz Tuck,Jong-Eun Park,Elior Rahmani,David Menon,OA Bayraktar,Kerstin Meyer,Peter Sims,Tong Li,Chuan Xu,Kourosh Saeb‐Parsy,Joanne Jones,Donna Farber,Krishnaa Mahbubani,Lorna Jarvis,Daniel Rainbow,Steven Wells,Tomás Gomes,S Howlett,Ondřej Suchánek,Krzysztof Polański,Hamish King,Lira Mamanova,Ni Huang,Peter Szabo,Laura Richardson,Liam Bolt,Eirini Fasouli,Martin Prete,Elizabeth Tuck,Nathan Richoz,Zewen Tuong,LS Campos,Hani Mousa,Edward Needham,Sophie Pritchard,Rasa Elmentaite,David Chen,Ömer Bayraktar,Louisa James,Nir Yosef,Menna Clatworthy
+81 authors
,Sarah Teichmann
Journal
Published
May 12, 2022
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Abstract

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

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